[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not Found
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not Found
File Not Found
They can use multiple cuvettes to do their readings faster (i.e. have 9 or 10 of the same cuvettes instead of washing one multiple times)
Make them save their spectrophotometer file – NameEnzymeAssayDATE
Make them save their spectrophotometer file – NameEnzymeAssayDATE
Make them save their spectrophotometer file – NameEnzymeAssayDATE
MAKE sure they clean up afterwards before you sign them out.
VS3 lab
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Protein Characterization Lab
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not Found
Tips & Hints
they need to have all 3 titrations on the same graph in the end - to do so, they will need to creat 3 calculated volume columns and give them each a different name (e.g. CV1, CV2, and CV3).
PyMol2
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not Found
Tips & Hints
show them how to use UT Webspacehttps://webspace.utexas.edu/xythoswfs/. to save their Image (.png) and Session (.pse) files. The first time they use it the have to 'sign up' on the Sign Up page.
Also there is an 'Advanced Upload' button that lets them have a drag and drop folder instead of uploading each file individually. (Much faster).
Beer's Law
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not Found
Tips & Hints
warm up specs for about 10 minutes before use
Henry spec reads very high on the Absorbance values - need to make sure they don't record their data if it is saturating the dector (>1.5 or 2 on the absorbance units)
Students should empty their cuvettes between EACH reading (i.e. for n=3 replicates, they shoudl empty the cuvette 3 times).
This takes longer but reinforces that just hitting the COLLECT button 3 times on the exact same sample does not constitute a true replicate.
To speed things up - they can get 3 cuvettes at a time and fill with a given dilution (Dil1, Dil2, Dil3, etc.)
-- then measure 3 in a row quickly.
They don't have to measure Dilution 1 - IF they know it is going to be above 1.5 Absorbance units.
Tips & Hints
Lab Notebook should include
Lab Safety - no liquids in lab to prevent electrocution
Materials - computer, PyMol program, helix.pdb, Betasheet.pdb
Figure captions - should include "carbons as green, oxygens as red, nitrogens as blue ....... etc. "
Timestamp for Word: ALT + i together, release and hit T Date Stamp for Excel: CTRL + ; Time Stamp for Excel: CTRL + SHFT + :
Show them how to do CROP in Word - to resize images.
When measuring across the helix for the diameter, they won't be able to go directly across the width(it will be on an angle).
They should be sure to address this in their comments and/or error analysis.
Teaching Points For VDS Spring 2012 Labs
Enzyme Assay Lab
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not Found[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not Found
They can use multiple cuvettes to do their readings faster (i.e. have 9 or 10 of the same cuvettes instead of washing one multiple times)
Make them save their spectrophotometer file – NameEnzymeAssayDATE
Make them save their spectrophotometer file – NameEnzymeAssayDATE
Make them save their spectrophotometer file – NameEnzymeAssayDATE
MAKE sure they clean up afterwards before you sign them out.
VS3 lab
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not FoundProtein Characterization Lab
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not FoundTeachingPointsMentors_CharacterizationLab.docx
Virtual Screening 2
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not FoundTeachingPointsMentors_VS2lab.docx
Protein Purification Lab
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not FoundTeachingPointsMentors_PurificationLab.docx
Virtual Screening 1
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not FoundTeachingPointsMentors_VS1lab.docx
16dhfr-ligsX.sdf
BasicLinux.pdf
Protein Expression
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not FoundPyMol3
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not FoundDHFR-hs.pdb
dhfr-lc.pdb
Buffer Titration
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not FoundTeachingPointsMentors_BufferTitration.docx
Henderson-Hasselbalch exercise answer sheet (password protected).VDS_6thClassJTB_Spring12Henderson-HasselbalchExercisesForSTAFF.docx
Tips & Hints
they need to have all 3 titrations on the same graph in the end - to do so, they will need to creat 3 calculated volume columns and give them each a different name (e.g. CV1, CV2, and CV3).
PyMol2
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not FoundTeachingPointsMentors_PyMol2.docx
DHFR-hs.pdb
Helix.pdb
Tips & Hints
show them how to use UT Webspacehttps://webspace.utexas.edu/xythoswfs/. to save their Image (.png) and Session (.pse) files. The first time they use it the have to 'sign up' on the Sign Up page.
Also there is an 'Advanced Upload' button that lets them have a drag and drop folder instead of uploading each file individually. (Much faster).
Beer's Law
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not FoundTeachingPointsMentors_BeersLaw.docx
Tips & Hints
warm up specs for about 10 minutes before use
Henry spec reads very high on the Absorbance values - need to make sure they don't record their data if it is saturating the dector (>1.5 or 2 on the absorbance units)
Students should empty their cuvettes between EACH reading (i.e. for n=3 replicates, they shoudl empty the cuvette 3 times).
This takes longer but reinforces that just hitting the COLLECT button 3 times on the exact same sample does not constitute a true replicate.
To speed things up - they can get 3 cuvettes at a time and fill with a given dilution (Dil1, Dil2, Dil3, etc.)
-- then measure 3 in a row quickly.
They don't have to measure Dilution 1 - IF they know it is going to be above 1.5 Absorbance units.
PyMOL1
TeachingPointsMentors_PyMol1.docx
this one is locked with the Mentor password (ask another mentor if you can't remember it!)
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not FoundBetaSheet.pdb
Helix.pdb
Tips & Hints
Lab Notebook should include
Lab Safety - no liquids in lab to prevent electrocution
Materials - computer, PyMol program, helix.pdb, Betasheet.pdb
Figure captions - should include "carbons as green, oxygens as red, nitrogens as blue ....... etc. "
Timestamp for Word: ALT + i together, release and hit T
Date Stamp for Excel: CTRL + ;
Time Stamp for Excel: CTRL + SHFT + :
Show them how to do CROP in Word - to resize images.
When measuring across the helix for the diameter, they won't be able to go directly across the width(it will be on an angle).
They should be sure to address this in their comments and/or error analysis.
Beer's Law
PyMol 2
Buffer Titration
PyMol 3
Old.....